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Manganese in PDB 5fh3: The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp

Enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp, PDB code: 5fh3 was solved by T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.66 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.699, 119.313, 60.821, 90.00, 107.95, 90.00
R / Rfree (%) 20.5 / 24.3

Other elements in 5fh3:

The structure of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp (pdb code 5fh3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp, PDB code: 5fh3:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5fh3

Go back to Manganese Binding Sites List in 5fh3
Manganese binding site 1 out of 3 in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:18.2
occ:1.00
 OD1 A:ASP311 1.6 7.6 0.3
O4 A:OXL703 1.9 22.3 1.0
O1G A:GTP704 2.1 17.3 0.7
O3 A:OXL703 2.2 18.9 1.0
NE2 A:HIS264 2.3 13.6 1.0
OD1 A:ASP311 2.4 18.5 0.7
NZ A:LYS244 2.5 19.1 1.0
O1G A:GTP704 2.6 8.9 0.3
CG A:ASP311 2.7 9.1 0.3
C2 A:OXL703 2.7 24.1 1.0
C1 A:OXL703 2.8 23.7 1.0
OD2 A:ASP311 3.2 8.8 0.3
PG A:GTP704 3.2 18.5 0.7
CD2 A:HIS264 3.2 14.2 1.0
CE1 A:HIS264 3.3 13.9 1.0
CG A:ASP311 3.4 17.9 0.7
O2G A:GTP704 3.6 17.7 0.7
CE A:LYS244 3.6 21.2 1.0
OD2 A:ASP311 3.6 18.0 0.7
PG A:GTP704 3.7 8.7 0.3
O2 A:OXL703 3.9 26.9 1.0
NZ A:LYS290 3.9 16.9 0.7
O3G A:GTP704 4.0 19.5 0.7
CB A:ASP311 4.0 9.4 0.3
O1 A:OXL703 4.1 25.0 1.0
O3G A:GTP704 4.1 9.1 0.3
CE A:LYS290 4.2 8.1 0.3
O A:HOH805 4.2 19.5 1.0
O A:HOH908 4.2 19.7 1.0
NZ A:LYS290 4.2 8.0 0.3
O2G A:GTP704 4.3 9.1 0.3
CE A:LYS290 4.3 16.5 0.7
ND1 A:HIS264 4.4 13.8 1.0
CG A:HIS264 4.4 13.6 1.0
O3B A:GTP704 4.5 18.9 0.7
CA A:ASP311 4.6 9.9 0.3
CB A:ASP311 4.8 18.1 0.7
O A:ASP311 4.8 11.3 0.3
CB A:SER286 4.9 23.1 0.7
O A:HOH1056 4.9 39.8 1.0
CD A:LYS244 5.0 20.2 1.0
CZ A:PHE485 5.0 19.1 1.0

Manganese binding site 2 out of 3 in 5fh3

Go back to Manganese Binding Sites List in 5fh3
Manganese binding site 2 out of 3 in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:17.9
occ:0.70
 MN A:MN702 0.0 17.9 0.7
MN A:MN702 1.3 6.3 0.3
OG1 A:THR291 1.7 8.9 0.3
O A:HOH817 1.9 22.3 1.0
O A:HOH805 2.0 19.5 1.0
OG1 A:THR291 2.1 16.3 0.7
O3G A:GTP704 2.2 19.5 0.7
O1B A:GTP704 2.2 17.7 0.7
OD2 A:ASP310 2.5 8.3 0.3
O A:HOH815 2.5 25.8 1.0
O1B A:GTP704 3.0 9.1 0.3
CB A:THR291 3.2 8.8 0.3
CG A:ASP310 3.2 8.2 0.3
O3G A:GTP704 3.3 9.1 0.3
CB A:THR291 3.3 16.6 0.7
PG A:GTP704 3.3 18.5 0.7
PB A:GTP704 3.4 18.6 0.7
O A:ASP310 3.5 8.5 0.3
OD2 A:ASP310 3.6 17.2 0.7
O3B A:GTP704 3.6 18.9 0.7
OD1 A:ASP310 3.8 8.1 0.3
CB A:ASP310 3.9 8.2 0.3
CA A:THR291 3.9 8.7 0.3
O1G A:GTP704 3.9 17.3 0.7
CG2 A:THR291 4.0 8.8 0.3
N A:THR291 4.0 8.5 0.3
O A:HOH908 4.0 19.7 1.0
O1A A:GTP704 4.0 22.4 0.7
N A:THR291 4.1 16.8 0.7
C A:ASP310 4.2 8.7 0.3
CA A:THR291 4.2 16.2 0.7
O A:ASP310 4.3 16.2 0.7
NH1 A:ARG405 4.3 21.2 0.7
PB A:GTP704 4.3 8.9 0.3
PG A:GTP704 4.4 8.7 0.3
CG2 A:THR291 4.4 16.5 0.7
CG A:ASP310 4.4 17.1 0.7
O2B A:GTP704 4.4 18.8 0.7
OD1 A:ASP311 4.5 18.5 0.7
O3A A:GTP704 4.5 19.3 0.7
CA A:GLY334 4.5 17.3 0.7
O A:HOH966 4.6 27.5 1.0
O2G A:GTP704 4.6 17.7 0.7
CA A:GLY334 4.6 7.0 0.3
O1G A:GTP704 4.6 8.9 0.3
N A:VAL335 4.7 16.4 0.7
CB A:ASP311 4.7 9.4 0.3
CA A:ASP310 4.7 8.2 0.3
O A:HOH818 4.7 27.7 1.0
O3B A:GTP704 4.7 8.9 0.3
PA A:GTP704 4.8 22.9 0.7
O A:PHE333 4.9 17.2 0.7
OD1 A:ASP311 4.9 7.6 0.3
CB A:LYS290 4.9 8.3 0.3
CB A:LYS290 4.9 16.6 0.7
C A:LYS290 4.9 8.4 0.3
O A:PHE333 5.0 6.9 0.3
N A:ASP311 5.0 9.4 0.3

Manganese binding site 3 out of 3 in 5fh3

Go back to Manganese Binding Sites List in 5fh3
Manganese binding site 3 out of 3 in the The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Rat Cytosolic Pepck Variant E89A in Complex with Oxalic Acid and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:6.3
occ:0.30
 MN A:MN702 0.0 6.3 0.3
MN A:MN702 1.3 17.9 0.7
O3G A:GTP704 1.5 19.5 0.7
O1B A:GTP704 1.8 17.7 0.7
O A:HOH815 1.9 25.8 1.0
O1B A:GTP704 2.1 9.1 0.3
O3G A:GTP704 2.2 9.1 0.3
OG1 A:THR291 2.2 8.9 0.3
PG A:GTP704 2.5 18.5 0.7
O3B A:GTP704 2.6 18.9 0.7
PB A:GTP704 2.6 18.6 0.7
O A:HOH817 2.6 22.3 1.0
O A:HOH805 2.7 19.5 1.0
OG1 A:THR291 3.2 16.3 0.7
O1A A:GTP704 3.2 22.4 0.7
PG A:GTP704 3.3 8.7 0.3
PB A:GTP704 3.3 8.9 0.3
CB A:THR291 3.4 8.8 0.3
O1G A:GTP704 3.5 17.3 0.7
O3A A:GTP704 3.5 19.3 0.7
O3B A:GTP704 3.6 8.9 0.3
O2G A:GTP704 3.6 17.7 0.7
OD2 A:ASP310 3.7 8.3 0.3
PA A:GTP704 3.8 22.9 0.7
NH1 A:ARG405 3.8 21.2 0.7
O1G A:GTP704 3.9 8.9 0.3
O2B A:GTP704 4.0 18.8 0.7
O1A A:GTP704 4.0 9.1 0.3
CB A:THR291 4.1 16.6 0.7
N A:THR291 4.1 8.5 0.3
CG2 A:VAL335 4.1 18.4 0.7
N A:VAL335 4.2 16.4 0.7
CA A:THR291 4.3 8.7 0.3
NH1 A:ARG405 4.3 8.4 0.3
O A:HOH908 4.4 19.7 1.0
O2B A:GTP704 4.4 8.8 0.3
O2A A:GTP704 4.4 20.3 0.7
O3A A:GTP704 4.4 9.0 0.3
CG2 A:THR291 4.4 8.8 0.3
CA A:GLY334 4.4 7.0 0.3
O A:ASP310 4.4 8.5 0.3
CG A:ASP310 4.5 8.2 0.3
O A:HOH818 4.5 27.7 1.0
N A:THR291 4.6 16.8 0.7
O2G A:GTP704 4.6 9.1 0.3
CB A:VAL335 4.7 18.2 0.7
N A:VAL335 4.7 7.3 0.3
CA A:GLY334 4.7 17.3 0.7
PA A:GTP704 4.8 9.2 0.3
CZ A:ARG405 4.8 21.4 0.7
O A:PHE333 4.9 6.9 0.3
OD2 A:ASP310 4.9 17.2 0.7
OD1 A:ASP311 4.9 18.5 0.7
CB A:LYS290 4.9 8.3 0.3
CA A:THR291 5.0 16.2 0.7
NH2 A:ARG405 5.0 20.9 0.7
O3 A:OXL703 5.0 18.9 1.0

Reference:

T.A.Johnson, M.J.Mcleod, T.Holyoak. Utilization of Substrate Intrinsic Binding Energy For Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Biochemistry V. 55 575 2016.
ISSN: ISSN 0006-2960
PubMed: 26709450
DOI: 10.1021/ACS.BIOCHEM.5B01215
Page generated: Sat Aug 16 17:24:11 2025

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